1
|
Yang X, Porcel E, Marichal L, Gonzalez-Vargas C, Khitous A, Salado-Leza D, Li X, Renault JP, Pin S, Remita H, Wien F, Lacombe S. Human Serum Albumin in the Presence of Small Platinum Nanoparticles. J Pharm Sci 2024; 113:1645-1652. [PMID: 38336007 DOI: 10.1016/j.xphs.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Noble metal materials, especially platinum nanoparticles (Pt NPs), have immense potential in nanomedicine as therapeutic agents on account of their high electron density and their high surface area. Intravenous injection is proposed as the best mode to deliver the product to patients. However, our understanding of the reaction of nanoparticles with blood components, especially proteins, is far behind the explosive development of these agents. Using synchrotron radiation circular dichroism (SRCD), we investigated the structural and stability changes of human serum albumin (HSA) upon interaction with PEG-OH coated Pt NPs at nanomolar concentrations, conditions potentially encountered for intravenous injection. There is no strong complexation found between HSA and Pt NPs. However, for the highest molar ratio of NP:HSA of 1:1, an increase of 18 °C in the thermal unfolding of HSA was observed, which is attributed to increased thermal stability of HSA generated by preferential hydration. This work proposes a new and fast method to probe the potential toxicity of nanoparticles intended for clinical use with intravenous injection.
Collapse
Affiliation(s)
- Xiaomin Yang
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Erika Porcel
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Cesar Gonzalez-Vargas
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Amine Khitous
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France; Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Daniela Salado-Leza
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France; CONAHCYT, Institute of Physics, Autonomous University of San Luis Potosi, 78295 San Luis Potosi, Mexico
| | - Xue Li
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Hynd Remita
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Frank Wien
- Synchrotron Soleil, 91190 Saint-Aubin, France.
| | - Sandrine Lacombe
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| |
Collapse
|
2
|
Garbagnoli M, Linciano P, Listro R, Rossino G, Vasile F, Collina S. Biophysical Assays for Investigating Modulators of Macromolecular Complexes: An Overview. ACS OMEGA 2024; 9:17691-17705. [PMID: 38680367 PMCID: PMC11044174 DOI: 10.1021/acsomega.4c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Drug discovery is a lengthy and intricate process, and in its early stage, crucial steps are the selection of the therapeutic target and the identification of novel ligands. Most targets are dysregulated in pathogenic cells; typically, their activation or deactivation leads to the desired effect, while in other cases, interfering with the target-natural binder complex achieves the therapeutic results. Biophysical assays are a suitable strategy for finding new ligands or interferent agents, being able to evaluate ligand-protein interactions and assessing the effect of small molecules (SMols) on macromolecular complexes. This mini-review provides a detailed analysis of widely used biophysical methods, including fluorescence-based approaches, circular dichroism, isothermal titration calorimetry, microscale thermophoresis, and NMR spectroscopy. After a brief description of the methodologies, examples of interaction and competition experiments are described, together with an analysis of the advantages and disadvantages of each technique. This mini-review provides an overview of the most relevant biophysical technologies that can help in identifying SMols able not only to bind proteins but also to interfere with macromolecular complexes.
Collapse
Affiliation(s)
- Martina Garbagnoli
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Pasquale Linciano
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Roberta Listro
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Giacomo Rossino
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Francesca Vasile
- Department
of Chemistry, University of Milan, Via Golgi 19, Milano 20133, Italy
| | - Simona Collina
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| |
Collapse
|
3
|
Sanders E, Csondor R, Šulskis D, Baronaitė I, Smirnovas V, Maheswaran L, Horrocks J, Munro R, Georgiadou C, Horvath I, Morozova-Roche LA, Williamson PTF. The Stabilization of S100A9 Structure by Calcium Inhibits the Formation of Amyloid Fibrils. Int J Mol Sci 2023; 24:13200. [PMID: 37686007 PMCID: PMC10488161 DOI: 10.3390/ijms241713200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/04/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
The calcium-binding protein S100A9 is recognized as an important component of the brain neuroinflammatory response to the onset and development of neurodegenerative disease. S100A9 is intrinsically amyloidogenic and in vivo co-aggregates with amyloid-β peptide and α-synuclein in Alzheimer's and Parkinson's diseases, respectively. It is widely accepted that calcium dyshomeostasis plays an important role in the onset and development of these diseases, and studies have shown that elevated levels of calcium limit the potential for S100A9 to adopt a fibrillar structure. The exact mechanism by which calcium exerts its influence on the aggregation process remains unclear. Here we demonstrate that despite S100A9 exhibiting α-helical secondary structure in the absence of calcium, the protein exhibits significant plasticity with interconversion between different conformational states occurring on the micro- to milli-second timescale. This plasticity allows the population of conformational states that favour the onset of fibril formation. Magic-angle spinning solid-state NMR studies of the resulting S100A9 fibrils reveal that the S100A9 adopts a single structurally well-defined rigid fibrillar core surrounded by a shell of approximately 15-20 mobile residues, a structure that persists even when fibrils are produced in the presence of calcium ions. These studies highlight how the dysregulation of metal ion concentrations can influence the conformational equilibria of this important neuroinflammatory protein to influence the rate and nature of the amyloid deposits formed.
Collapse
Affiliation(s)
- Ella Sanders
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Rebecca Csondor
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Darius Šulskis
- Sector of Amyloid Research, Institute of Biotechnology, Life Sciences Centre, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Ieva Baronaitė
- Sector of Amyloid Research, Institute of Biotechnology, Life Sciences Centre, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Vytautas Smirnovas
- Sector of Amyloid Research, Institute of Biotechnology, Life Sciences Centre, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Luckshi Maheswaran
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Jack Horrocks
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Rory Munro
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Christina Georgiadou
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Istvan Horvath
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | | | | |
Collapse
|
4
|
Vanloon J, Bennett HA, Martin A, Wien F, Harroun T, Yan H. Synchrotron Radiation Circular Dichroism Spectroscopy of Oligonucleotides at Millimolar Concentrations. Bioorg Med Chem Lett 2023:129376. [PMID: 37328039 DOI: 10.1016/j.bmcl.2023.129376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/18/2023]
Abstract
Circular dichroism spectroscopy of nucleic acids has been traditionally performed at sample concentrations orders of magnitude lower than what occur in biological systems. While recent work from us demonstrated the flexibility of an adjustable sample cell that allowed for successful recording of CD spectra of an 18- and a 21-mer double stranded DNA sequences at around 1 mM, sample concentrations beyond 1 mM present a challenge for standard benchtop CD spectrometers. In the present work, the synchrotron radiation circular dichroism (SRCD) spectra were recorded for d(CG)9 and a mixed 18-mer double stranded DNA at 1, 5, and 10 mM in 100 mM or 4 M NaCl. SRCD of low molecular weight salmon DNA was also measured at a 10 mg/ml concentration. These results represent the first report of CD spectra of DNA samples measured at concentrations comparable to those found in the nucleus. The results suggest that dsDNA maintain very similar structures at concentrations up to 10s of mg/ml, as evident by the very similar CD patterns in this concentration range. Furthermore, the SRCD allowed for the recording of CD patterns of DNA in the far UV region, which is not readily accessible by standard benchtop CD spectropolarimeters. These far UV signals appear to be quite characteristic of DNA structures and are sensitive to sample conditions.
Collapse
Affiliation(s)
- Jesse Vanloon
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Hayley-Ann Bennett
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Alicia Martin
- Department of Physics, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192, Gif-sur-Yvette, France.
| | - Thad Harroun
- Department of Physics, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada.
| | - Hongbin Yan
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada.
| |
Collapse
|
5
|
Szpotkowski K, Wójcik K, Kurzyńska-Kokorniak A. Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques. Comput Struct Biotechnol J 2023; 21:2858-2872. [PMID: 37216015 PMCID: PMC10195699 DOI: 10.1016/j.csbj.2023.04.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Protein-nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge of the biological functions and molecular mechanisms beyond the activity of the macromolecular complexes can be determined from their tertiary structures. Undoubtably, performing structural studies of protein-nucleic acid complexes is challenging, mainly because these types of complexes are often unstable. In addition, their individual components may display extremely different surface charges, causing the complexes to precipitate at higher concentrations used in many structural studies. Due to the variety of protein-nucleic acid complexes and their different biophysical properties, no simple and universal guideline exists that helps scientists chose a method to successfully determine the structure of a specific protein-nucleic acid complex. In this review, we provide a summary of the following experimental methods, which can be applied to study the structures of protein-nucleic acid complexes: X-ray and neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force microscopy (AFM), small angle scattering (SAS) methods, circular dichroism (CD) and infrared (IR) spectroscopy. Each method is discussed regarding its historical context, advancements over the past decades and recent years, and weaknesses and strengths. When a single method does not provide satisfactory data on the selected protein-nucleic acid complex, a combination of several methods should be considered as a hybrid approach; thus, specific structural problems can be solved when studying protein-nucleic acid complexes.
Collapse
|
6
|
Karlsson E, Andersson E, Jones NC, Hoffmann SV, Jemth P, Kjaergaard M. Coupled Binding and Helix Formation Monitored by Synchrotron-Radiation Circular Dichroism. Biophys J 2019; 117:729-742. [PMID: 31378314 PMCID: PMC6712486 DOI: 10.1016/j.bpj.2019.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/29/2019] [Accepted: 07/10/2019] [Indexed: 01/27/2023] Open
Abstract
Intrinsically disordered proteins organize interaction networks in the cell in many regulation and signaling processes. These proteins often gain structure upon binding to their target proteins in multistep reactions involving the formation of both secondary and tertiary structure. To understand the interactions of disordered proteins, we need to understand the mechanisms of these coupled folding and binding reactions. We studied helix formation in the binding of the molten globule-like nuclear coactivator binding domain and the disordered interaction domain from activator of thyroid hormone and retinoid receptors. We demonstrate that helix formation in a rapid binding reaction can be followed by stopped-flow synchrotron-radiation circular dichroism (CD) spectroscopy and describe the design of such a beamline. Fluorescence-monitored binding experiments of activator of thyroid hormone and retinoid receptors and nuclear coactivator binding domain display several kinetic phases, including one concentration-independent phase, which is consistent with an intermediate stabilized at high ionic strength. Time-resolved CD experiments show that almost all helicity is formed upon initial association of the proteins or separated from the encounter complex by only a small energy barrier. Through simulation of mechanistic models, we show that the intermediate observed at high ionic strength likely involves a structural rearrangement with minor overall changes in helicity. Our experiments provide a benchmark for simulations of coupled binding reactions and demonstrate the feasibility of using synchrotron-radiation CD for mechanistic studies of protein-protein interactions.
Collapse
Affiliation(s)
- Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus, Denmark
| | | | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus, Denmark; Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
7
|
Witkowska D, Rowińska-Żyrek M. Biophysical approaches for the study of metal-protein interactions. J Inorg Biochem 2019; 199:110783. [PMID: 31349072 DOI: 10.1016/j.jinorgbio.2019.110783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.
Collapse
Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
| | | |
Collapse
|
8
|
Tanwar N, Munde M. Thermodynamic and conformational analysis of the interaction between antibody binding proteins and IgG. Int J Biol Macromol 2018; 112:1084-1092. [PMID: 29410106 DOI: 10.1016/j.ijbiomac.2018.01.208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/25/2018] [Accepted: 01/31/2018] [Indexed: 01/29/2023]
Abstract
Studying interaction of IgG with bacterial proteins such as proA (Protein A) and proG is essential for development in the areas of drug discovery and biotechnology. Some solution studies in the past have hinted at the possibility of variable binding ratios for IgG with proA and proG. Since earlier crystallographic studies focussed mostly on monomeric complexes, the knowledge about the binding interfaces and protein conformational changes involved in multimeric complexes is scarce. In this paper, we observed that single proA molecule was able to bind to three IgG molecules (1:3, proA:IgG) in ITC accentuating the presence of conformational flexibility in proA, corroborated also by CD results. By contrast, proG binds with 1:1 stoichiometry to IgG, which also involves key structural rearrangement within the binding interface of IgG-proG complex, confirmed by fluorescence KI quenching study. It is implicit from CD and fluorescence results that IgG does not undergo any significant conformational changes, which further suggests that proA and proG dictate the phenomenon of recognition in antibody complexes. ANS as a hydrophobic probe helped in revealing the distinctive antibody binding mechanism of proA and proG. Additionally, the binding competition experiments using ITC established that proA and proG cannot bind IgG concurrently.
Collapse
Affiliation(s)
- Neetu Tanwar
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| |
Collapse
|
9
|
Cloning, expression, and spectral analysis of mouse betatrophin. Med J Islam Repub Iran 2017; 31:102. [PMID: 29951403 PMCID: PMC6014755 DOI: 10.14196/mjiri.31.102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 12/18/2017] [Indexed: 12/11/2022] Open
Abstract
Background: Betatrophin, a novel secretory protein from liver and fatty tissues, is believed to be involved in lipid and glucose metabolism. However, its precise physiological role remains unclear. Here, we report the cloning, expression, and purification steps of mouse betatrophin in a prokaryotic system, followed by its structural analysis. Methods: Specific cloning primers were used to amplify the coding sequence of mouse liver betatrophin. The product was cloned into pET28 and expressed in E.coli BL21 (DE3) cells. The suitability of the refolding procedure was assessed by determining secondary structures of the initial and refolded proteins using circular dichroism spectroscopy. Results: The polymerase chain reaction resulted in a 549 bp nucleotide sequence, encoding a 183 amino acid polypeptide, with an apparent molecular weight of 21 kDa, which was expressed in an inclusion body. Following an optimization and refolding procedure, the recombinant protein was purified by anion exchange and metal affinity chromatography. CD spectra revealed that the refolded protein has suitable configuration. Conclusion: We believe that the produced betatrophin is suitable for further biochemical studies on glucose and lipid metabolism.
Collapse
|
10
|
Zhao J, Xu L, Liang Q, Sun Q, Chen C, Zhang Y, Ding Y, Zhou P. Metal chelator EGCG attenuates Fe(III)-induced conformational transition of α-synuclein and protects AS-PC12 cells against Fe(III)-induced death. J Neurochem 2017; 143:136-146. [PMID: 28792609 DOI: 10.1111/jnc.14142] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022]
Abstract
The fibrillation and aggregation of α-synuclein (AS), along with the conformational transition from random coil to β-sheet, are the critical steps in the development of Parkinson's disease (PD). It is acknowledged that iron accumulation in the brain may lead to the fibrillation of AS. However, (-)-epigallocatechin gallate (EGCG) can penetrate the blood-brain barrier, chelate metal ions, and inhibit the fibrillation of amyloid proteins. Therefore, EGCG is warranted to be investigated for its potential to cure amyloid-related diseases. In the present work, we sought to study the effects of EGCG on Fe(III)-induced fibrillation of AS on both molecular and cellular levels. We demonstrate that Fe(III) interacts with the amino residue of Tyr and Ala of AS, then accelerates the fibrillation of AS, and increases intracellular reactive oxygen species (ROS) in the AS transduced-PC12 cells (AS-PC12 cells). However, EGCG significantly inhibits this process by chelating Fe(III) and protects AS-PC12 cells against the toxicity induced by ROS and β-sheet-enriched AS fibrils. These findings yield useful information that EGCG might be a promising drug to prevent and treat the neurodegenerative diseases.
Collapse
Affiliation(s)
- Juan Zhao
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Lihui Xu
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Qingnan Liang
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Qing Sun
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Congheng Chen
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Yuan Zhang
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - Yu Ding
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ping Zhou
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| |
Collapse
|
11
|
Wang K, Sun DW, Pu H, Wei Q. Principles and applications of spectroscopic techniques for evaluating food protein conformational changes: A review. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.06.015] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
12
|
Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J 2017. [PMID: 28636916 DOI: 10.1016/j.bpj.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.
Collapse
|
13
|
Afonin S, Kubyshkin V, Mykhailiuk PK, Komarov IV, Ulrich AS. Conformational Plasticity of the Cell-Penetrating Peptide SAP As Revealed by Solid-State 19F-NMR and Circular Dichroism Spectroscopies. J Phys Chem B 2017; 121:6479-6491. [PMID: 28608690 DOI: 10.1021/acs.jpcb.7b02852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cell-penetrating peptide SAP, which was designed as an amphipathic poly-l-proline helix II (PPII), was suggested to self-assemble into regular fibrils that are relevant for its internalization. Herein we have analyzed the structure of SAP in the membrane-bound state by solid-state 19F-NMR, which revealed other structural states, in addition to the expected surface-aligned PPII. Trifluoromethyl-bicyclopentyl-glycine (CF3-Bpg) and two rigid isomers of trifluoromethyl-4,5-methanoprolines (CF3-MePro) were used as labels for 19F-NMR analysis. The equilibria between different conformations of SAP were studied and were found to be shifted by the substituents at Pro-11. Synchrotron-CD results suggested that substituting Pro-11 by CF3-MePro governed the coil-to-PPII equilibrium in solution and in the presence of a lipid bilayer. Using CD and 19F-NMR, we examined the slow kinetics of the association of SAP with membranes and the dependence of the SAP conformational dynamics on the lipid composition. The peptide did not bind to lipids in the solid ordered phase and aggregated only in the liquid ordered "raft"-like bilayers. Self-association could not be detected in solution or in the presence of liquid disordered membranes. Surface-bound amphipathic SAP in a nonaggregated state was structured as a mixture of nonideal extended conformations reflecting the equilibrium already present in solution, i.e., before binding to the membrane.
Collapse
Affiliation(s)
- Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology , P.O.B. 3640, 76021 Karlsruhe, Germany
| | - Vladimir Kubyshkin
- Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Pavel K Mykhailiuk
- Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.,Enamine Ltd. , Vul. Chervonotkatska 78, 02660 Kyiv, Ukraine
| | - Igor V Komarov
- Institute of High Technologies, Taras Shevchenko National University of Kyiv , Prosp. Glushkova 4-g, 02033 Kyiv, Ukraine
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology , P.O.B. 3640, 76021 Karlsruhe, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| |
Collapse
|
14
|
Bortolini C, Liu L, Hoffmann SV, Jones NC, Knowles TPJ, Dong M. Exciton Coupling of Phenylalanine Reveals Conformational Changes of Cationic Peptides. ChemistrySelect 2017. [DOI: 10.1002/slct.201601916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Christian Bortolini
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds vej 14 8000 Aarhus Denmark
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Lei Liu
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds vej 14 8000 Aarhus Denmark
| | - Søren V. Hoffmann
- ISA, Department of Physics and AstronomyAarhus University Ny Munkegade 120 8000 Aarhus Denmark
| | - Nykola C. Jones
- ISA, Department of Physics and AstronomyAarhus University Ny Munkegade 120 8000 Aarhus Denmark
| | - Tuomas P. J. Knowles
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds vej 14 8000 Aarhus Denmark
| |
Collapse
|
15
|
Advantages of synchrotron radiation circular dichroism spectroscopy to study intrinsically disordered proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:599-606. [PMID: 28258312 DOI: 10.1007/s00249-017-1202-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others. Using synchrotron radiation as the light source for CD spectroscopy represents the state-of-the-art version of this technique with feasibility of accessing the lower wavelength UV region, and therefore presenting a series of advantages over conventional circular dichroism (cCD) to monitor a protein conformational behavior, check protein stability, detect ligand binding, and many others. In this paper, we have performed a comparative study using cCD and SRCD methods for investigating the secondary structure and the conformational behavior of natively unfolded proteins: MEG-14 and soybean trypsin inhibitor. We show that the SRCD technique greatly improves the analysis and accuracy of the studies on the conformations of IDPs.
Collapse
|
16
|
Gold nanoparticles increases UV and thermal stability of human serum albumin. Biointerphases 2016; 11:04B310. [PMID: 27984858 DOI: 10.1116/1.4972113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ultraviolet (UV) radiation, temperature, and time can degrade proteins. Here, the authors show that gold nanoparticles significantly protect human serum albumin from denaturation when exposed to "stressing" conditions such as UV irradiation and sustained exposure in suboptimal conditions. In particular, the authors show that gold nanoparticles significantly reduce the decrease in secondary structure induced by UV irradiation or extended exposure to ambient temperature.
Collapse
|
17
|
Savoie JD, Otis F, Bürck J, Ulrich AS, Voyer N. Crown ether helical peptides are preferentially inserted in lipid bilayers as a transmembrane ion channels. Biopolymers 2016; 104:427-33. [PMID: 25753314 DOI: 10.1002/bip.22633] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/18/2015] [Accepted: 02/23/2015] [Indexed: 11/08/2022]
Abstract
Oriented circular dichroism was used to study the alignment crown ether-modified peptides. The influence of different N- and C-functionalities was assessed using at variable peptide:lipid ratios from 1:20 to 1:200. Neither the functionalities nor the concentration had any major effect on the orientation. The alignment of the 21-mer peptides was also examined with lipid membranes of different bilayer thickness. The use of synchrotron radiation as light source allowed the study of peptide:lipid molar ratios from 1:20 to 1:1000. For all conditions studied, the peptides were found to be predominantly incorporated as a transmembrane helix into the membrane, especially at low peptide concentration, but started to aggregate on the membrane surface at higher peptide:lipid ratios. The structural information on the preferred trans-bilayer alignment of the crown ether functional groups explains their ion conductivity and is useful for the further development of membrane-active nanochemotherapeutics.
Collapse
Affiliation(s)
- Jean-Daniel Savoie
- Faculté des Sciences et de Génie, Département de chimie and PROTEO, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - François Otis
- Faculté des Sciences et de Génie, Département de chimie and PROTEO, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Normand Voyer
- Faculté des Sciences et de Génie, Département de chimie and PROTEO, Université Laval, Québec, QC, G1V 0A6, Canada
| |
Collapse
|
18
|
Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
Collapse
Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
| |
Collapse
|
19
|
Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
Collapse
Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
| |
Collapse
|
20
|
Deller MC, Kong L, Rupp B. Protein stability: a crystallographer's perspective. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:72-95. [PMID: 26841758 PMCID: PMC4741188 DOI: 10.1107/s2053230x15024619] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.
Collapse
Affiliation(s)
- Marc C Deller
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125, USA
| | - Leopold Kong
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084, USA
| |
Collapse
|
21
|
Asghari H, Chegini KG, Amini A, Gheibi N. Effect of poly and mono-unsaturated fatty acids on stability and structure of recombinant S100A8/A9. Int J Biol Macromol 2015; 84:35-42. [PMID: 26642838 DOI: 10.1016/j.ijbiomac.2015.11.065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 11/21/2015] [Accepted: 11/23/2015] [Indexed: 12/21/2022]
Abstract
Recombinant pET 15b vectors containing the coding sequences S100A8 and S100A9 are expressed in Escherichia coli BL21 (DE3) and purified using Ni-NTA affinity chromatography. The structural changes of S100A8/A9 complex are analyzed upon interaction with poly/mono-unsaturated fatty acids (UFAs). The thermodynamic values, Gibbs free energy and the protein melting point, are obtained through thermal denaturation of protein both with and without UFAs by thermal scanning of protein emission using the fluorescence spectroscopy technique. The far-ultraviolet circular dichroism spectra show that all studied unsaturated fatty acids, including arachidonic, linoleic, alpha-linolenic and oleic acids, induce changes in the secondary structure of S100A8/A9 by reducing the α-helix and β-sheet structures. The tertiary structure of S100A8/A9 has fluctuations in the fluorescence emission spectra after the incubation of protein with UFAs. The blue-shift of emission maximum wavelength and the increase in fluorescence intensity of anilino naphthalene-8-sulfonic acid confirm that the partial unfolding is caused by the conformational changes in the tertiary structure in the presence of UFAs. The structural changes in S100A8/A9 and its lower stability in the presence of UFAs may be necessary for S100A8/A9 to play a biological role in the inflammatory milieu.
Collapse
Affiliation(s)
- Hamideh Asghari
- Department of Biotechnology, School of Para Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Koorosh Goodarzvand Chegini
- Department of Clinical Biochemistry and Genetics, School of Medicine, Qazvin University of Medical Science, Qazvin, Iran
| | - Abbas Amini
- School of Computing, Engineering and Mathematics, Western Sydney University, Bld Y, Locked Bag 1797, NSW 2751, Australia.
| | - Nematollah Gheibi
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, P.O. Box 34199-15315, Qazvin, Iran.
| |
Collapse
|
22
|
Bürck J, Roth S, Windisch D, Wadhwani P, Moss D, Ulrich AS. UV-CD12: synchrotron radiation circular dichroism beamline at ANKA. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:844-52. [PMID: 25931105 PMCID: PMC4416691 DOI: 10.1107/s1600577515004476] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/03/2015] [Indexed: 05/25/2023]
Abstract
Synchrotron radiation circular dichroism (SRCD) is a rapidly growing technique for structure analysis of proteins and other chiral biomaterials. UV-CD12 is a high-flux SRCD beamline installed at the ANKA synchrotron, to which it had been transferred after the closure of the SRS Daresbury. The beamline covers an extended vacuum-UV to near-UV spectral range and has been open for users since October 2011. The current end-station allows for temperature-controlled steady-state SRCD spectroscopy, including routine automated thermal scans of microlitre volumes of water-soluble proteins down to 170 nm. It offers an excellent signal-to-noise ratio over the whole accessible spectral range. The technique of oriented circular dichroism (OCD) was recently implemented for determining the membrane alignment of α-helical peptides and proteins in macroscopically oriented lipid bilayers as mimics of cellular membranes. It offers improved spectral quality <200 nm compared with an OCD setup adapted to a bench-top instrument, and accelerated data collection by a factor of ∼3. In addition, it permits investigations of low hydrated protein films down to 130 nm using a rotatable sample cell that avoids linear dichroism artifacts.
Collapse
Affiliation(s)
- Jochen Bürck
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Siegmar Roth
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Dirk Windisch
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - David Moss
- ANKA Synchrotron Radiation Facility, Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| |
Collapse
|
23
|
Manzo G, Scorciapino MA, Wadhwani P, Bürck J, Montaldo NP, Pintus M, Sanna R, Casu M, Giuliani A, Pirri G, Luca V, Ulrich AS, Rinaldi AC. Enhanced amphiphilic profile of a short β-stranded peptide improves its antimicrobial activity. PLoS One 2015; 10:e0116379. [PMID: 25617899 PMCID: PMC4305290 DOI: 10.1371/journal.pone.0116379] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 12/05/2014] [Indexed: 12/11/2022] Open
Abstract
SB056 is a novel semi-synthetic antimicrobial peptide with a dimeric dendrimer scaffold. Active against both Gram-negative and -positive bacteria, its mechanism has been attributed to a disruption of bacterial membranes. The branched peptide was shown to assume a β-stranded conformation in a lipidic environment. Here, we report on a rational modification of the original, empirically derived linear peptide sequence [WKKIRVRLSA-NH2, SB056-lin]. We interchanged the first two residues [KWKIRVRLSA-NH2, β-SB056-lin] to enhance the amphipathic profile, in the hope that a more regular β-strand would lead to a better antimicrobial performance. MIC values confirmed that an enhanced amphiphilic profile indeed significantly increases activity against both Gram-positive and -negative strains. The membrane binding affinity of both peptides, measured by tryptophan fluorescence, increased with an increasing ratio of negatively charged/zwitterionic lipids. Remarkably, β-SB056-lin showed considerable binding even to purely zwitterionic membranes, unlike the original sequence, indicating that besides electrostatic attraction also the amphipathicity of the peptide structure plays a fundamental role in binding, by stabilizing the bound state. Synchrotron radiation circular dichroism and solid-state 19F-NMR were used to characterize and compare the conformation and mobility of the membrane bound peptides. Both SB056-lin and β-SB056-lin adopt a β-stranded conformation upon binding POPC vesicles, but the former maintains an intrinsic structural disorder that also affects its aggregation tendency. Upon introducing some anionic POPG into the POPC matrix, the sequence-optimized β-SB056-lin forms well-ordered β-strands once electro-neutrality is approached, and it aggregates into more extended β-sheets as the concentration of anionic lipids in the bilayer is raised. The enhanced antimicrobial activity of the analogue correlates with the formation of these extended β-sheets, which also leads to a dramatic alteration of membrane integrity as shown by 31P-NMR. These findings are generally relevant for the design and optimization of other membrane-active antimicrobial peptides that can fold into amphipathic β-strands.
Collapse
Affiliation(s)
- Giorgia Manzo
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Mariano A. Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Nicola Pietro Montaldo
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Manuela Pintus
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Roberta Sanna
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Mariano Casu
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Andrea Giuliani
- Research & Development Unit, Spider Biotech S.r.l., I-10010 Colleretto Giacosa (TO), Italy
| | - Giovanna Pirri
- Research & Development Unit, Spider Biotech S.r.l., I-10010 Colleretto Giacosa (TO), Italy
| | - Vincenzo Luca
- Dipartimento di Scienze Biochimiche, “A. Rossi Fanelli”, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Andrea C. Rinaldi
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| |
Collapse
|
24
|
Lopes JL, Nobre TM, Cilli EM, Beltramini LM, Araújo AP, Wallace B. Deconstructing the DGAT1 enzyme: Binding sites and substrate interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3145-52. [DOI: 10.1016/j.bbamem.2014.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 11/28/2022]
|
25
|
Angelov B, Angelova A, Papahadjopoulos-Sternberg B, Hoffmann SV, Nicolas V, Lesieur S. Protein-Containing PEGylated Cubosomic Particles: Freeze-Fracture Electron Microscopy and Synchrotron Radiation Circular Dichroism Study. J Phys Chem B 2012; 116:7676-86. [DOI: 10.1021/jp303863q] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Borislav Angelov
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nam. 1888/2, Praha 6, Czech Republic
| | - Angelina Angelova
- CNRS UMR8612 Physico-chimie-Pharmacotechnie-Biopharmacie,
Univ Paris Sud 11, LabEx LERMIT, 92296
Châtenay-Malabry, France
| | | | - Søren V. Hoffmann
- Institute for Storage Ring Facilities
(ISA), Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - Valérie Nicolas
- Imaging platform, IFR141, Institut
Paris-Sud d’Innovation Thérapeutique (IPSIT), Univ Paris Sud 11, 92290 Châtenay-Malabry, France
| | - Sylviane Lesieur
- CNRS UMR8612 Physico-chimie-Pharmacotechnie-Biopharmacie,
Univ Paris Sud 11, LabEx LERMIT, 92296
Châtenay-Malabry, France
| |
Collapse
|
26
|
Brunet C, Antoine R, Allouche AR, Dugourd P, Canon F, Giuliani A, Nahon L. Gas phase photo-formation and vacuum UV photofragmentation spectroscopy of tryptophan and tyrosine radical-containing peptides. J Phys Chem A 2011; 115:8933-9. [PMID: 21744817 DOI: 10.1021/jp205617x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Tryptophan (Trp(•)) and tyrosyl (Tyr(•)) radical containing peptides were produced by UV laser-induced electron detachment from a suitable precursor. Vacuum ultraviolet (VUV) action spectra of these radical peptides were recorded with synchrotron radiation in the 4.5-16 eV range, from which fragmentation pathways and yields are measured as a function of the VUV photon energy. An enhancement in photofragmentation yields of radical species by 1 order of magnitude with respect to nonradical peptides is demonstrated here for the first time. Photofragmentation spectra are compared with absorption spectra for model chromophores calculated in the frame of the time-dependent density functional theory (TDDFT). A qualitative agreement in the position of bands in the 6-8 eV region is observed between experimental photofragmentation and calculated absorption spectra. Photofragmentation spectra of peptide radicals can be useful to better assess the complex deactivation pathways that occur following the absorption of a VUV photon in biomolecular radical anions.
Collapse
Affiliation(s)
- Claire Brunet
- Université de Lyon , F-69622, Lyon, France, Université Lyon 1, 69622 Villeurbanne Cedex, France
| | | | | | | | | | | | | |
Collapse
|
27
|
Travnikova O, Liu JC, Lindblad A, Nicolas C, Söderström J, Kimberg V, Gel'mukhanov F, Miron C. Circularly polarized x rays: another probe of ultrafast molecular decay dynamics. PHYSICAL REVIEW LETTERS 2010; 105:233001. [PMID: 21231455 DOI: 10.1103/physrevlett.105.233001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Indexed: 05/30/2023]
Abstract
Dissociative nuclear motion in core-excited molecular states leads to a splitting of the fragment Auger lines: the Auger-Doppler effect. We present here for the first time experimental evidence for an Auger-Doppler effect following F1s → a(1g)* inner-shell excitation by circularly polarized x rays in SF(6). In spite of a uniform distribution of the dissociating S-F bonds near the polarization plane of the light, the intersection between the subpopulation of molecules selected by the core excitation with the cone of dissociation induces a strong anisotropy in the distribution of the S-F bonds that contributes to the scattering profile measured in the polarization plane.
Collapse
Affiliation(s)
- Oksana Travnikova
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|